Kondō died of aortic dissection – alternately aneurysm[1] – in 1998. His death is said to have been caused by excess work and pressure from Isao Takahata[2], and seems to be the main reason for Hayao Miyazaki's first announcement of retirement in 1998. Although Miyazaki later returned to Studio Ghibli, Kondō's death seems to have influenced Miyazaki to work at a more relaxed pace.

In 1978, he co-authored a textbook for beginning animators titled Animation Book (アニメーションの本 Animēshon no Hon). He moved to Telecom Animation Film on December 16, 1980, where he worked as the character designer for Sherlock Hound. On March 16, 1985, Kondō resigned his position at Telecom Animation Film, and was hospitalized from June through August for a type of pneumonia (自然気胸 shizen kikyō). He Became a contract worker for Nippon Animation afterwards and moved to Studio Ghibli in January, 1987. In 1995, he made his directorial debut with the film Whisper of the Heart. On January 21, 1998, he died suddenly of an aortic dissection in the Tachikawa City Hospital in Tokyo at age 47.